AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana

RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtR...

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Detalles Bibliográficos
Autores: Zhang, Runxuan, Calixto, Cristiane P. G., Tzioutziou, Nikoleta A., James, Allan B., Simpson, Craig G., Guo, Wenbin, Marquez, Yamile, Kalyna, Maria, Patro, Rob, Eyras Jiménez, Eduardo, Barta, Andrea, Nimmo, Hugh G., Brown, John W. S.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2015
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/25817
Acceso en línea:http://hdl.handle.net/10230/25817
http://dx.doi.org/10.1111/nph.13545
Access Level:acceso abierto
Palabra clave:RNA
Alternative splicing
Arabidopsis thaliana
High resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq)
SAILFISH
SALMON
Transcripts per million
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spelling AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thalianaZhang, RunxuanCalixto, Cristiane P. G.Tzioutziou, Nikoleta A.James, Allan B.Simpson, Craig G.Guo, WenbinMarquez, YamileKalyna, MariaPatro, RobEyras Jiménez, EduardoBarta, AndreaNimmo, Hugh G.Brown, John W. S.RNAAlternative splicingArabidopsis thalianaHigh resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq)SAILFISHSALMONTranscripts per millionRNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes Sailfish and Salmon and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.This research was supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/K006568/1 to J.W.S.B.; BB/K006835/1 to H.G.N.), the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) and by the Austrian Science Fund (FWF) (P26333) to M.K. and (DK W1207) to A.B. The authors acknowledge the European Alternative Splicing Network of Excellence (EURASNET), LSHG-CT-2005-518238 for catalysing important collaborations.Wiley201620162015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/25817http://dx.doi.org/10.1111/nph.13545reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésNew Phytologist. 2015;208(1):96-101© 2015 New Phytologist Trust. This is an open access article under the terms of the Creative Commons Attribution License, which permits use,/ndistribution and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/258172026-05-29T05:05:01Z
dc.title.none.fl_str_mv AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
title AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
spellingShingle AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
Zhang, Runxuan
RNA
Alternative splicing
Arabidopsis thaliana
High resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq)
SAILFISH
SALMON
Transcripts per million
title_short AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
title_full AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
title_fullStr AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
title_full_unstemmed AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
title_sort AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
dc.creator.none.fl_str_mv Zhang, Runxuan
Calixto, Cristiane P. G.
Tzioutziou, Nikoleta A.
James, Allan B.
Simpson, Craig G.
Guo, Wenbin
Marquez, Yamile
Kalyna, Maria
Patro, Rob
Eyras Jiménez, Eduardo
Barta, Andrea
Nimmo, Hugh G.
Brown, John W. S.
author Zhang, Runxuan
author_facet Zhang, Runxuan
Calixto, Cristiane P. G.
Tzioutziou, Nikoleta A.
James, Allan B.
Simpson, Craig G.
Guo, Wenbin
Marquez, Yamile
Kalyna, Maria
Patro, Rob
Eyras Jiménez, Eduardo
Barta, Andrea
Nimmo, Hugh G.
Brown, John W. S.
author_role author
author2 Calixto, Cristiane P. G.
Tzioutziou, Nikoleta A.
James, Allan B.
Simpson, Craig G.
Guo, Wenbin
Marquez, Yamile
Kalyna, Maria
Patro, Rob
Eyras Jiménez, Eduardo
Barta, Andrea
Nimmo, Hugh G.
Brown, John W. S.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv RNA
Alternative splicing
Arabidopsis thaliana
High resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq)
SAILFISH
SALMON
Transcripts per million
topic RNA
Alternative splicing
Arabidopsis thaliana
High resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq)
SAILFISH
SALMON
Transcripts per million
description RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes Sailfish and Salmon and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.
publishDate 2015
dc.date.none.fl_str_mv 2015
2016
2016
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/25817
http://dx.doi.org/10.1111/nph.13545
url http://hdl.handle.net/10230/25817
http://dx.doi.org/10.1111/nph.13545
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv New Phytologist. 2015;208(1):96-101
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.81155

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